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Quantification of growth and nutrient consumption of bacterial and fungal cultures in microfluidic microhabitat models

Arellano-Caicedo, Carlos LU ; Beech, Jason P. LU ; Bengtsson, Martin LU ; Ohlsson, Pelle LU orcid and Hammer, Edith C. LU (2024) In STAR Protocols 5(1).
Abstract

Understanding microbes in nature requires consideration of their microenvironment. Here, we present a protocol for quantifying biomass and nutrient degradation of bacterial and fungal cultures (Pseudomonas putida and Coprinopsis cinerea, respectively) in microfluidics. We describe steps for mask design and fabrication, master printing, polydimethylsiloxane chip fabrication, and chip inoculation and imaging using fluorescence microscopy. We include procedures for image analysis, plotting, and statistics. For complete details on the use and execution of this protocol, please refer to Arellano-Caicedo et al. (2023).1

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author
; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Environmental sciences, Microbiology, Microscopy
in
STAR Protocols
volume
5
issue
1
article number
102784
publisher
Cell Press
external identifiers
  • pmid:38103191
  • scopus:85180278168
ISSN
2666-1667
DOI
10.1016/j.xpro.2023.102784
language
English
LU publication?
yes
additional info
Funding Information: The authors acknowledge funding from the Swedish Research Council ( VR-621-2014-5912 ), the Foundation for Strategic Research (future research leader grant SSF FFL18-0089 ), and the strategic research environment BECC . We thank Sam Bengtsson Gartner, Stephanie Casey, Saleh Moradi, and Ara Fadel Hamid for their assistance with device mass fabrication, microscopy, and image analysis. Funding Information: The authors acknowledge funding from the Swedish Research Council (VR-621-2014-5912), the Foundation for Strategic Research (future research leader grant SSF FFL18-0089), and the strategic research environment BECC. We thank Sam Bengtsson Gartner, Stephanie Casey, Saleh Moradi, and Ara Fadel Hamid for their assistance with device mass fabrication, microscopy, and image analysis. E.C.H. and C.A.-C. conceived the idea, developed the protocol design, and wrote the manuscript. C.A.-C. designed and manufactured the chips, performed the experiments, and developed the data analysis. P.O. assisted in the development of the microfluidic designs, methods, data analysis, and data interpretation. M.B. developed an adjusted protocol for the mask design and manufacturing. J.P.B. developed an adjusted protocol for the masters manufacturing. All authors contributed with the exchange of ideas and reviewed the manuscript. The authors declare no competing interests. Publisher Copyright: © 2023
id
bcab0304-7be2-4a89-82dc-17ebe15204e3
date added to LUP
2024-01-02 16:51:28
date last changed
2024-04-17 16:00:22
@article{bcab0304-7be2-4a89-82dc-17ebe15204e3,
  abstract     = {{<p>Understanding microbes in nature requires consideration of their microenvironment. Here, we present a protocol for quantifying biomass and nutrient degradation of bacterial and fungal cultures (Pseudomonas putida and Coprinopsis cinerea, respectively) in microfluidics. We describe steps for mask design and fabrication, master printing, polydimethylsiloxane chip fabrication, and chip inoculation and imaging using fluorescence microscopy. We include procedures for image analysis, plotting, and statistics. For complete details on the use and execution of this protocol, please refer to Arellano-Caicedo et al. (2023).<sup>1</sup></p>}},
  author       = {{Arellano-Caicedo, Carlos and Beech, Jason P. and Bengtsson, Martin and Ohlsson, Pelle and Hammer, Edith C.}},
  issn         = {{2666-1667}},
  keywords     = {{Environmental sciences; Microbiology; Microscopy}},
  language     = {{eng}},
  month        = {{03}},
  number       = {{1}},
  publisher    = {{Cell Press}},
  series       = {{STAR Protocols}},
  title        = {{Quantification of growth and nutrient consumption of bacterial and fungal cultures in microfluidic microhabitat models}},
  url          = {{http://dx.doi.org/10.1016/j.xpro.2023.102784}},
  doi          = {{10.1016/j.xpro.2023.102784}},
  volume       = {{5}},
  year         = {{2024}},
}